One complicating factor I think for Fallout is that the world is supposed to be really, really scary and dangerous out there. Not that Skyrim or Morrowind, say, were paradises, but the post-apocalyptic wastelands are seriously dangerous places. Fast travel is weird for me mostly because it completely removes a major aspect of the world, the danger of traveling “on the surface,” from the perspective of a vault dweller for instance.
I mean, you have every third person it seems being a murderous raider. There are roaming feral ghouls all over. You have mutated animals that can rip your limbs clean off. You have robots that have gone bonkers, crazed fanatics with power armor, murderous synths, and trigger-happy caravan guards. You have radiation all over the place, and in Fallout 4 you even have an attempt at STALKER-style radiation storms. Travel in this environment is a challenge, and some of the best parts of the game come from trying to get to your next quest location only to find you can’t get there from here, directly, so you work your way around to where you’re going, having to dodge or avoid or kill the above mentioned obstacles.
In this environment, “fast travel” is hard to reconcile, thematically or contextually. As a game mechanic catering to player tastes, it works (hell, I confess, I’m a filthy fast-travel using heathen most of the time), but it totally breaks the lore. For instance, walking from Southie to Sanctuary is not a trek for the faint of heart. Caravans coming up from Quincy, say, take guards and are often attacked on the way. You, though, can always get home safe and sound, even loaded to the gills with more valuable stuff than any ten caravans, because you can teleport there effectively. Hmm, now that’s a late-game possibility, but no matter. The point is, I do definitely see the problem here. It makes no sense that you can safely and instantly pop back and forth from a lore standpoint. That is not to say from a game mechanics/player satisfaction point of view what they’re doing is wrong, though. I’m pretty sure the vast majority of players would balk at a more “realistic” or lore-centered travel system, and making it optional wouldn’t really be better than having a mod. From a design POV, it should be integral to the worldbuilding.
Wastelands 2, though a very different sort of game, doesn’t allow you to fast travel, though it abstracts the process because the game world is literally not a world but a collection of zones loosely linked by overland travel through, well, a wasteland. Fast travel there would not make much sense, even though you rarely come across much in the Wastelands that is interesting. In Fallout 4, there is so much stuff everywhere that you always miss out on something when you fast travel. After a while, the stuff you’re missing diminishes to mostly the radiant/random stuff, but that still argues strongly for a travel system that scales with game progression. Early on, there should be zero fast travel. You’re fresh out of a vault, you’re literally just thawed out, and you are freakin’ clueless about this not-so brave new world. As you get stronger, know more people, learn the new landscape, etc., your options should increase. Pay a caravan to join it, or serve as a guard, for instance. Eventually, your faction rewards should include various forms of fast travel, as is already done to an extent. By the time you’re pretty much just tooling around like the angel of death, sure, full fast travel would make sense. If you can one-shot alpha Deathclaws, no one is going to mess with you. But when you come out of the vault with a pistol and an ugly blue suit? Not so much.
tl;dr, for me, it doesn’t affect my enjoyment of the game (124 hours and counting), but I have to agree that the world design is, well, inconsistent and in some ways sloppy. I truly admire much of what is being done, and the game has an astounding amount of mostly really nice content. It’s the context, and the way it’s all woven together, that sort of falls down. Bethesda has demonstrated time and again that they can build the components of a world. What they have not mastered is weaving it all together into the world itself, and fast travel is one bit of evidence for that failing.